Brown joined York after leaving Halifax in September 2020 and was part of the squad that sealed promotion into the National League through the play-offs, beating Boston United in the final.
Brown made 139 appearances over four seasons with the Shaymen, helping them win the FA Trophy in 2016 and promotion into the fifth tier a year later.
Brown posted on Twitter: "My time at York City is up. 3rd career promotion achieved. Met some unbelievable genuine people at the club and I wish them all the very best in the future. Time for a new project."